Complexity of Viral Epitope Surfaces as Evasive Targets for Vaccines and Therapeutic Antibodies

Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination

(2022) Katharina Röltgen et al.   CELL

Exploring the role of framework mutations in enabling breadth of a cross-reactive antibody (CR3022) against the SARS-CoV-2 RBD and its variants of concern

(2022) Samvedna Saini et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The origin of SARS-CoV-2 variants of concern

(2022) Talha Burki   LANCET INFECTIOUS DISEASES

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

(2022) Elisabetta Cameroni et al.   NATURE

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

(2022) Sandile Cele et al.   NATURE

Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies

(2022) Yunlong Cao et al.   NATURE

Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2

(2022) Lihong Liu et al.   NATURE

Results of a phase 1, randomized, placebo-controlled first-in-human trial of griffithsin formulated in a carrageenan vaginal gel

(2022) Natalia Teleshova et al.   PLoS One

Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes

(2022) Juan Rodriguez-Rivas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches

(2022) Wei Yu et al.   Viruses-Basel

SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy

(2022) Ziwei Yang et al.   mBio

Conserved topology of virus glycoepitopes presents novel targets for repurposing HIV antibody 2G12

(2022) Nathaniel L. Miller et al.   Scientific Reports

SARS-CoV-2 vaccination washes away original antigenic sin

(2022) Shiv Pillai   TRENDS IN IMMUNOLOGY

Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody

(2021) C. Garrett Rappazzo et al.   SCIENCE

Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies

(2021) Maxwell T. Finkelstein et al.   Viruses-Basel

Molecular determinants and mechanism for antibody cocktail preventing SARS-CoV-2 escape

(2021) Zhiqiang Ku et al.   Nature Communications

Dissecting strategies to tune the therapeutic potential of SARS-CoV-2–specific monoclonal antibody CR3022

(2021) Caroline Atyeo et al.   JCI Insight

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

(2021) Wilfredo F. Garcia-Beltran et al.   CELL

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

(2021) Allison J. Greaney et al.   Cell Host & Microbe

SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations

(2021) Gennady M. Verkhivker et al.   BIOCHEMISTRY

Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization

(2021) Pengfei Wang et al.   Cell Host & Microbe

Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma

(2021) Sandile Cele et al.   NATURE

Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection

(2021) David S. Khoury et al.   NATURE MEDICINE

Computational epitope map of SARS-CoV-2 spike protein

(2021) Mateusz Sikora et al.   PLoS Computational Biology

A cross-neutralizing antibody between HIV-1 and influenza virus

(2021) Chang-Chun D. Lee et al.   PLoS Pathogens

A human coronavirus evolves antigenically to escape antibody immunity

(2021) Rachel T. Eguia et al.   PLoS Pathogens

Mechanisms of Hepatitis C Virus Escape from Vaccine-Relevant Neutralizing Antibodies

(2021) Rodrigo Velázquez-Moctezuma et al.   Vaccines

Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations

(2021) Frauke Muecksch et al.   IMMUNITY

Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species

(2021) Ruoke Wang et al.   IMMUNITY

SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern

(2021) Alice Triveri et al.   Journal of Chemical Information and Modeling

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection

(2021) Zijun Wang et al.   NATURE

High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape

(2021) Fabian Schmidt et al.   NATURE

A glycan gate controls opening of the SARS-CoV-2 spike protein

(2021) Terra Sztain et al.   Nature Chemistry

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies

(2021) Allison J. Greaney et al.   Nature Communications

One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening

(2021) Irene M. Francino-Urdaniz et al.   Cell Reports

Comprehensive Deep Mutational Scanning Reveals the Immune-Escaping Hotspots of SARS-CoV-2 Receptor-Binding Domain Targeting Neutralizing Antibodies

(2021) Keng-Chang Tsai et al.   Frontiers in Microbiology

SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution

(2021) Jiří Zahradník et al.   Nature Microbiology

Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment

(2021) Liang Chen et al.   mSphere

Glycans in Virus-Host Interactions: A Structural Perspective

(2021) Nathaniel L. Miller et al.   Frontiers in Molecular Biosciences

Where did ‘weird’ Omicron come from?

(2021) Kai Kupferschmidt   SCIENCE

An Antigenic Space Framework for Understanding Antibody Escape of SARS-CoV-2 Variants

(2021) Nathaniel L. Miller et al.   Viruses-Basel

Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies

(2021) Erik Laurini et al.   Scientific Reports

A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo

(2020) Evelyn M. Covés-Datson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody

(2020) Xiaolong Tian et al.   Emerging Microbes & Infections

Rational Vaccine Design in the Time of COVID-19

(2020) Dennis R. Burton et al.   Cell Host & Microbe

Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches

(2020) Sepideh Parvizpour et al.   DRUG DISCOVERY TODAY

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

(2020) Meng Yuan et al.   SCIENCE

Networks of HIV-1 Envelope Glycans Maintain Antibody Epitopes in the Face of Glycan Additions and Deletions

(2020) Gemma E. Seabright et al.   STRUCTURE

Nipah Virus: Past Outbreaks and Future Containment

(2020) Vinod Soman Pillai et al.   Viruses-Basel

Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition

(2020) Jason Gorman et al.   Cell Reports

Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model

(2020) Jae-Keun Park et al.   NATURE MEDICINE

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

Prediction of the binding interface between monoclonal antibody m102.4 and Nipah attachment glycoprotein using structure-guided alanine scanning and computational docking

(2020) Phanthakarn Tit-oon et al.   Scientific Reports

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

(2020) Allison J. Greaney et al.   Cell Host & Microbe

Antigenic variation of SARS‐CoV‐2 in response to immune pressure

(2020) Diego Forni et al.   MOLECULAR ECOLOGY

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

(2020) Nicholas C. Wu et al.   PLoS Pathogens

VH1-69 antiviral broadly neutralizing antibodies: genetics, structures, and relevance to rational vaccine design

(2019) Fang Chen et al.   Current Opinion in Virology

Influenza Antigen Engineering Focuses Immune Responses to a Subdominant but Broadly Protective Viral Epitope

(2019) Goran Bajic et al.   Cell Host & Microbe

Human Influenza A Virus Hemagglutinin Glycan Evolution Follows a Temporal Pattern to a Glycan Limit

(2019) Meghan O. Altman et al.   mBio

Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan

(2019) Jeffrey Umotoy et al.   IMMUNITY

Rational design of Zika virus subunit vaccine with enhanced efficacy

(2019) Wanbo Tai et al.   JOURNAL OF VIROLOGY

Repeat vaccination reduces antibody affinity maturation across different influenza vaccine platforms in humans

(2019) Surender Khurana et al.   Nature Communications

Affinity maturation in a human humoral response to influenza hemagglutinin

(2019) Kevin R. McCarthy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Immune Recognition of the HIV Glycan Shield

(2018) Max Crispin et al.   Annual Review of Biophysics

Rational Engineering and Characterization of an mAb that Neutralizes Zika Virus by Targeting a Mutationally Constrained Quaternary Epitope

(2018) Kannan Tharakaraman et al.   Cell Host & Microbe

Antibody Immunodominance: The Key to Understanding Influenza Virus Antigenic Drift

(2018) Meghan O. Altman et al.   VIRAL IMMUNOLOGY

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

(2018) Jared Adolf-Bryfogle et al.   PLoS Computational Biology

Human dengue virus serotype 2 neutralizing antibodies target two distinct quaternary epitopes

(2018) Emily N. Gallichotte et al.   PLoS Pathogens

Antibody-mediated protection against Ebola virus

(2018) Erica Ollmann Saphire et al.   NATURE IMMUNOLOGY

Cross reactivity of commercial anti-dengue immunoassays in patients with acute Zika virus infection

(2017) Alvina Clara Felix et al.   JOURNAL OF MEDICAL VIROLOGY

Antibody-dependent enhancement of severe dengue disease in humans

(2017) Leah C. Katzelnick et al.   SCIENCE

Staged induction of HIV-1 glycan–dependent broadly neutralizing antibodies

(2017) Mattia Bonsignori et al.   Science Translational Medicine

Epitope and Paratope Mapping Reveals Temperature-Dependent Alterations in the Dengue-Antibody Interface

(2017) Xin-Xiang Lim et al.   STRUCTURE

A single mutation in the envelope protein modulates flavivirus antigenicity, stability, and pathogenesis

(2017) Leslie Goo et al.   PLoS Pathogens

Humoral cross-reactivity between Zika and dengue viruses: implications for protection and pathology

(2017) Lalita Priyamvada et al.   Emerging Microbes & Infections

Molecular basis of antibody-mediated neutralization and protection against flavivirus

(2016) Lianpan Dai et al.   IUBMB LIFE

Dengue virus sero-cross-reactivity drives antibody-dependent enhancement of infection with zika virus

(2016) Wanwisa Dejnirattisai et al.   NATURE IMMUNOLOGY

SAbPred: a structure-based antibody prediction server

(2016) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting

(2016) Katelyn M. Gostic et al.   SCIENCE

Specificity, cross-reactivity, and function of antibodies elicited by Zika virus infection

(2016) K. Stettler et al.   SCIENCE

Griffithsin: An Antiviral Lectin with Outstanding Therapeutic Potential

(2016) Sabrina Lusvarghi et al.   Viruses-Basel

Composition and Antigenic Effects of Individual Glycan Sites of a Trimeric HIV-1 Envelope Glycoprotein

(2016) Anna-Janina Behrens et al.   Cell Reports

Structure-Guided Design of an Anti-dengue Antibody Directed to a Non-immunodominant Epitope

(2015) Luke N. Robinson et al.   CELL

Engineering a Therapeutic Lectin by Uncoupling Mitogenicity from Antiviral Activity

(2015) Michael D. Swanson et al.   CELL

The HIV glycan shield as a target for broadly neutralizing antibodies

(2015) Katie J. Doores   FEBS Journal

New Member of the V1V2-Directed CAP256-VRC26 Lineage That Shows Increased Breadth and Exceptional Potency

(2015) Nicole A. Doria-Rose et al.   JOURNAL OF VIROLOGY

Antiviral drug discovery: broad-spectrum drugs from nature

(2015) J. P. Martinez et al.   NATURAL PRODUCT REPORTS

Estimating the Life Course of Influenza A(H3N2) Antibody Responses from Cross-Sectional Data

(2015) Adam J. Kucharski et al.   PLOS BIOLOGY

Structural Evolution of Glycan Recognition by a Family of Potent HIV Antibodies

(2014) Fernando Garces et al.   CELL

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

(2014) Nicole A. Doria-Rose et al.   NATURE

Activity of and Effect of Subcutaneous Treatment with the Broad-Spectrum Antiviral Lectin Griffithsin in Two Laboratory Rodent Models

(2013) Christopher Barton et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring

(2013) Brian Jiménez-García et al.   BIOINFORMATICS

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

Rational Engineering of a Human Anti-Dengue Antibody through Experimentally Validated Computational Docking

(2013) Luca Simonelli et al.   PLoS One

Antiviral Lectins from Red and Blue-Green Algae Show Potent In Vitro and In Vivo Activity against Hepatitis C Virus

(2013) Yutaka Takebe et al.   PLoS One

A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein

(2013) Anurag Sethi et al.   PLoS Computational Biology

Cooperativity Between CD8+ T Cells, Non-Neutralizing Antibodies, and Alveolar Macrophages Is Important for Heterosubtypic Influenza Virus Immunity

(2013) Brian J. Laidlaw et al.   PLoS Pathogens

Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans

(2013) Jean-Philippe Julien et al.   PLoS Pathogens

Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity

(2012) C. M. Midgley et al.   JOURNAL OF IMMUNOLOGY

Molecular Mechanisms Involved in Antibody-Dependent Enhancement of Dengue Virus Infection in Humans

(2012) Jacky Flipse et al.   TRAFFIC

Flavivirus-induced antibody cross-reactivity

(2011) K. L. Mansfield et al.   JOURNAL OF GENERAL VIROLOGY

Mechanism of Neutralization by the Broadly Neutralizing HIV-1 Monoclonal Antibody VRC01

(2011) Y. Li et al.   JOURNAL OF VIROLOGY

Broad neutralization coverage of HIV by multiple highly potent antibodies

(2011) Laura M. Walker et al.   NATURE

A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield

(2011) R. Pejchal et al.   SCIENCE

Networks link antigenic and receptor-binding sites of influenza hemagglutinin: Mechanistic insight into fitter strain propagation

(2011) Venkataramanan Soundararajan et al.   Scientific Reports

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Correlates of Protection Induced by Vaccination

(2010) S. A. Plotkin   Clinical and Vaccine Immunology

Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1

(2010) R. Pejchal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

(2010) T. Zhou et al.   SCIENCE

Cross-Reacting Antibodies Enhance Dengue Virus Infection in Humans

(2010) W. Dejnirattisai et al.   SCIENCE

Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target

(2009) L. M. Walker et al.   SCIENCE

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Structural Insights into the Mechanisms of Antibody-Mediated Neutralization of Flavivirus Infection: Implications for Vaccine Development

(2008) Theodore C. Pierson et al.   Cell Host & Microbe